'''
Created on May 6, 2011

@author: oabalbin
'''


# intersect tumor vs normal variant
# Anotate variants using vcfCodings
# Produce a list of "Non-synonymous" variants
# Output a concensus snp table using the two algorithms and the actionable genes.
from collections import defaultdict
from exome.variantEval.variant_intersector import SNPs_isec

def intersect_somatic_benign(analysis, configrun, jobrunfunc):
    '''
    Find the intersection between two files: one of tumor snvs
    and one of benign snvs.
    '''
    
    tumor_snvs, benign_snvs,
    
    cohort_samples = defaultdict
    
    for sp in analysis.samples:
        patient_id
        if sp.category=='benign':
            cohort_samples['benign'].append(sp.sorted_mmarkdup_bam)
        else:
            cohort_samples['tumor'].append(sp.sorted_mmarkdup_bam)

    
    
    <patient_id>mdapca183a_organism</patient_id>
    do_complement, output_vcf_file
    
    
    
 





